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Sample GSM989740 Query DataSets for GSM989740
Status Public on Aug 23, 2012
Title PC 45T
Sample type RNA
 
Channel 1
Source name reference RNA
Organism Homo sapiens
Characteristics reference: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PC 45T2
Organism Homo sapiens
Characteristics ethnicity: Caucasian
age: 56
pre-operation treatment: None
individual: PC 455T
disease free survival: 49.13
tissue: prostate
Growth protocol All prostate samples used for this study were collected at the Stanford University Medical Center between 1999 and 2007 with patient's informed consent under an Institutional Review Board (IRB)-approved protocol. Multiple tissue samples were harvested from each prostate, flash-frozen and stored at 80oC. Frozen sections of each prostate sample were performed and evaluated by a genitourinary pathologist (JKM). The tumor and nontumor areas were marked and contaminating tissues were trimmed away from the block as described previously.48 Tumor samples in which at least 90% of the epithelial cells were cancerous were selected for extraction of DNA and RNA. In total, we selected 98 tumors from 86 patients that met these criteria. Associated clinical data were collected and included preoperative PSA levels, clinical stage, pathological stage, tumor Gleason grade and clinical follow-up. Recurrence was defined as a measurable serum PSA (>0.1ng/ml on two consecutive measurements) after surgery.
Gene-expression profiling was performed as reported. Briefly, Cy5-labeled cDNA was prepared by using 50ug of total RNA from prostate samples and Cy3-labeled cDNA was prepared by using common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines. For each experimental sample, Cy5- and Cy3-labeled samples were cohybridized to HEEBO spotted microarrays.49 HEEBO microarrays were manufactured in the Stanford Functional Genomics Facility at Stanford University and contained 44-544 70-mer probes.
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol After hybridization, microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments-Molecular Devices, LLC, Sunnyvale, CA, USA). Fluorescence ratios for array elements were extracted using GENEPIX software and uploaded into the Stanford Microarray Database for subsequent analysis.
Description Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81123.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 21, 2012
Last update date Aug 23, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL15973
Series (1)
GSE40272 Gene-expression profiling of prostate tumors

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 15621 12690 91 226 15530 12463 15974 12448 119 308 15883 12221 0 0 2603 1789 158 350 100 100 100 100 27993 28104 1.246 .803 .769 .809 .766 2.098 32 227 .755 .97 70 2450 6670 23 30 41 48 0 10421 186 10235 .659 10222 10036 1.517 .632 -.602 -.662
2 16143 13127 89 246 16054 12881 17247 13695 130 319 17158 13449 0 0 4127 2399 197 349 100 100 100 100 28935 30607 1.246 .802 .784 .824 .787 2.04 32 176 .775 .99 60 2600 6670 24 30 57 63 0 10780 202 10578 .659 11246 11044 1.518 .644 -.602 -.636
3 15027 32941 94 230 14932 32711 21011 44132 113 273 20916 43901 0 0 10073 21120 82 183 82 96 76 90 47643 64817 .456 2.191 2.099 3.426 2.224 5.352 52 340 2.142 .99 90 2750 6670 22 31 70 79 0 27051 189 26862 1.799 36241 36051 .556 1.724 .847 .785
4 15445 11914 90 235 15355 11678 16518 13035 103 277 16428 12800 0 0 4403 4108 60 184 100 100 100 100 27033 29228 1.315 .761 .779 .718 .766 2.397 52 262 .767 .98 80 2910 6670 23 31 87 95 0 9784 193 9590 .625 10704 10511 1.601 .64 -.679 -.644
5 532 358 90 252 442 106 592 349 107 286 502 96 0 0 243 159 58 163 87 31 87 15 548 598 4.17 .24 .191 .264 .324 5.72 32 170 .25 .27 60 3050 6660 23 29 102 108 0 294 207 87 .197 287 79 5.078 .157 -2.344 -2.671
6 9426 14821 189 308 9236 14512 9821 14390 213 349 9631 14081 0 0 2395 4326 126 252 100 100 100 100 23748 23712 .636 1.571 1.462 1.586 1.547 2.275 52 242 1.597 .97 80 3210 6680 24 32 117 125 0 12171 253 11917 1.29 11817 11563 .775 1.201 .368 .264
7 211 222 106 261 104 -39 206 205 143 312 99 -56 0 0 96 130 108 253 44 1 13 0 65 43 null null null .704 .712 8.812 52 295 4.996 .29 90 3350 6660 21 30 130 139 -50 182 214 -32 null 168 -46 null null null null
8 15190 34134 93 266 15096 33867 24107 51918 109 306 24013 51651 0 0 12997 27275 67 196 75 78 65 78 48963 75664 .446 2.243 2.151 3.627 2.279 4.851 52 323 2.16 .99 90 3500 6660 21 30 145 154 0 28031 218 27811 1.842 42635 42415 .543 1.766 .882 .821
9 168 240 102 238 65 2 142 205 113 294 40 -32 0 0 101 167 71 314 34 7 17 1 67 8 32.5 .031 null 1.787 1.596 7.571 52 333 7.177 .5 90 3660 6660 21 30 161 170 -50 197 195 2 .025 168 -26 39.577 null -5.307 null
10 1114 355 106 229 1008 126 982 320 126 295 876 91 0 0 601 191 79 355 96 15 96 1 1134 967 8 .125 .104 .175 .163 8.156 52 248 .097 .21 80 3820 6670 23 31 178 186 0 292 188 103 .103 263 75 9.742 .085 -3.284 -3.551
11 566 1418 104 225 461 1193 595 1357 120 251 490 1132 0 0 197 488 59 138 96 100 90 100 1654 1622 .386 2.588 2.31 2.797 2.725 3.372 32 163 2.762 .82 60 3960 6670 24 30 193 199 0 1164 185 980 2.125 1114 930 .471 1.897 1.088 .924
12 482 1130 98 263 383 867 472 1198 113 359 374 935 0 0 163 429 87 776 96 56 90 3 1250 1309 .442 2.264 2.5 2.185 2.212 3.312 32 227 3.954 .62 70 4110 6660 22 29 207 214 0 928 216 712 1.859 984 768 .538 2.053 .894 1.038
13 314 332 80 236 233 95 297 314 95 302 216 77 0 0 107 208 57 379 96 9 84 0 328 293 2.453 .408 .356 .653 .753 5.863 32 227 .362 .1 70 4260 6660 22 29 222 229 0 273 194 78 .335 258 63 2.987 .293 -1.579 -1.772
14 312 425 79 252 233 172 320 420 93 286 240 167 0 0 120 162 55 188 91 41 75 16 405 407 1.355 .738 .696 .882 1.138 10.16 12 104 1.157 .44 50 4420 6660 23 28 239 244 0 349 207 141 .606 345 137 1.65 .571 -.722 -.807
15 87 143 80 263 6 -119 77 133 95 306 -3 -129 0 0 40 79 64 239 5 0 1 0 -113 -132 null null null 5.248 6.015 8.356 52 317 8.618 .37 90 4560 6660 21 30 251 260 -50 117 216 -98 null 109 -106 null null null null
16 1943 2324 80 251 1862 2073 1988 2320 95 286 1907 2069 0 0 462 629 77 191 100 100 100 100 3935 3976 .898 1.113 1.085 1.102 1.136 2.243 32 221 1.12 .91 70 4710 6660 22 29 267 274 0 1908 206 1702 .914 1905 1699 1.094 .891 -.129 -.167
17 181 435 81 232 99 202 170 384 92 291 88 151 0 0 64 172 52 204 66 33 41 16 301 239 .49 2.04 1.716 1.719 1.668 6.057 12 68 3.752 .36 40 4860 6670 25 29 284 288 0 357 191 166 1.676 315 124 .597 1.409 .745 .495
18 70 158 79 218 -9 -60 70 143 93 268 -9 -74 0 0 26 94 76 239 0 0 0 0 -69 -83 null null null 6.047 5.93 6.433 52 323 9.95 .45 90 5010 6660 21 30 296 305 -50 130 179 -49 null 117 -61 null null null null
19 395 515 81 232 313 282 404 501 93 281 323 268 0 0 162 209 73 205 92 63 82 19 595 591 1.11 .901 .83 .942 .897 5.019 52 319 1.317 .36 90 5170 6660 21 30 312 321 0 423 191 232 .74 411 220 1.352 .681 -.435 -.554
20 1858 7309 74 219 1784 7089 1854 7358 84 265 1780 7138 0 0 394 1290 37 159 100 100 100 100 8873 8918 .252 3.974 4.01 4.006 4.149 2.112 32 203 3.971 .97 70 5320 6670 23 30 328 335 0 6002 180 5821 3.263 6042 5862 .306 3.293 1.706 1.719

Total number of rows: 44544

Table truncated, full table size 9823 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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